u/Firm-Panic7608

Considering we see simple villages and a bunch of abandoned temples all over the place, it's likely that the world used to house a much bigger civilization, but it disappeared, and likely took out a large chunk of the world's biosphere with it. Yet, surviving populations of wildlife existed in small pockets all over the world.

It is just that Minecraft's world is so impossibly large that it takes forever for any specific species to migrate anywhere. The players live in an ecological dead zone, but as years are passing by, more species are starting to reach and repopulate the vacant lands. These new species of plant and animal are in turn responsible for all the new biomes we see.